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Kura clover on Menfro silt loam in Chariton County, Missouri 2006

Microorganisms and Soil Health

Doran et al. 1994.

Nmin; Nitrate, Ammonium. Nmin

Aggregate Stability

P mineralization, solubilization

Active C

Microbial groups are associated with other soil health indicators

Microbial involvement in stable aggregate formation

1) Microfauna (< 0.1mm), -protozoa

2) Mesofauna (0.1 - 2mm), - mites, collembolans, and nematodes

3) Macrofauna (>2mm), (oligochaetes earthworms).

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Importance:Biological activities in soils:

Highly sensitive to soil-altering processes (degradative or beneficial); Changes can guide appropriate management (conservation or restoration practices in response to degradation; validation of GMP in practice)

Indicators: measures that collectively suggest whether or not soil is functioning normally

Development / identification of a standard set of biological soil health indicators has been elusive.

Major difficulty in use organisms and activities to assess soil health = methodological.

Biological Attributes of Soil Health

Microbial Ecology Interactions SOIL - Biologically dynamic system

Biological attributes interact with physical and chemical properties• Aggregate Stability

activity and products of organisms contribute to aggregation; water transport, low erosion, microbial habitat, C storage• Soil Organic Matter (C fractions)

key factors influencing biological activity and result of microbial activity, soil structure, soil fertility, plant nutrition

• Soil Enzyme Activity

Soil microbial activity, nutrient transformation, decomposition; influenced by soil nutrient status, vegetation,

management

Microbial Indicators of Soil Health 

Microbial Biomass – very general indicatorEnzyme ActivitiesSoil Respiration, N transformations (‘Greenhouse gasses’?)Microbial Characterization

C Utilization ProfilesFatty acid ProfilesNucleic Acid Profiles

Selected “soil fauna” *ORGANIC MATTER (CARBON)

– influences many readily measurable soil functions and processes; soil microorganisms closely associated w/ “active

fraction of SOM”*Aggregate Stability

*Intimately related to soil biological processes

No consensus in defining specific parameters for inclusion in data set for Soil Health assessment

Complete data set on microbial portion of Soil Health is lacking

Need: Identify minimum number of parameters that considers processes as well as community diversity for successful establishment of biotic component in determining Soil Health

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Few Biological Indicators can be Field Measured --

Soil respiration (CO2 efflux) - indicator of biological activity (SQI 2001)Draeger Tube - color change shows relative amount CO2

(appropriate conversion factor(s) allow calculation of soil microbial biomass C)

Microbial biomass => indicates potential ‘turnover’ rate relative to amount of N mineralized - tends to decline under degradation

Solvita “Soil Life Kit” - gel indicator color change (24-hr incubation), qualitative indicator of respiration; expensive

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Phospholipid Fatty Acid Methyl Ester (PFLA)• PLFA found only in living cells – PFLA profiles provide measure of soil microbial

diversity• Specific PLFA patterns detected via gas chromatography yield information on soil

microbial community shifts and structure• “Peaks” indicate “biomarkers” for specific soil microbial groups

http://www.microbe.com/plfa.html

Carbon chain lengths of 12-20 carbons are generally associated with microorganisms. Fatty acids designated by the number of carbon atoms, followed by a colon, the number of double bonds, and then position of the first double bond from the methyl (ω) end of the molecules. Branched fatty acids are indicated by ‘i’ and ‘a’ for iso and anteiso branching, respectively.

Unger et al. 2013. Agroforestry Systems

How can Soil Microbial status of soil be expressed?

1. “Total Living Microbial Biomass” - ng/g, nmol or pmol units

Example: 1400 - 6700 ng/g soil for 240 Missouri soybean fields

Implications:

“Soil Microbial Biomass”• Labile (living) component of the soil organic fraction• 1 – 3% of the total soil organic C• ≤ 5% of the total soil N • Contributes to potential Nmin pool: [30 - 60 lbs/A for SOM 2.65 - 5.3%]• “activity” is mediated by the diverse soil microbial community• Involved in nutrient fluxes, decomposition, plant growth regulation• Sensitive indicator of changes in managed and natural ecosystems –

major soil quality/health parameter

• No indication of function or activity

How can Soil Microbial status of soil be expressed?

2.“Diversity Index” -

A diversity index is a quantitative measure that reflects how many different types (such as microbial species - ‘biomarkers’) are present in sample.

Index value increases when number of types increase and evenness (how close in numbers each species in an environment are) increases.

Index value is maximized when all types are equally abundant.

Diversity index ranged from 1.5 to 3.5 for soils from 240 Missouri soybean fields (2011).

- Similarity index: comparing the similarity of soils

- Implications:- High of soil microbial diversity assures functional activity is near optimum- (activity of microbial ‘consortia’ in place)

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Indices for describing soil microbial abundance and diversity

Values reflect microbial community characteristics

Diversity index (various) - assess composition diversitySpecies richness (abundance) - numbers of different speciesSpecies evenness - distribution of individuals within species

Greater diversity => greater ability of soil to accommodate all critical functions necessary for healthy condition

Certain Management (i.e., Cover Cropping, Managed Grazing, etc.) can foster Biodiversity -

Reduce externalities (inputs)Reduce pollutionBenefit vegetative and soil biological diversity

*Use of diversity measurement in Soil Health assessment is still in fluxSoil Quality (Health) concept advanced in early 1990’sSoil microbial diversity beginnings in 1980’s but is constantly

evolving to present day - We have opportunity to demonstrate value of this indicator to

overall soil health assessment

Soil Microbial Categories:3. “Total Bacteria” -

(ng/g; nmol/g, pmol/g, mol%)

- Gram negative Overall: plant health, nutrient cycling

N transformations:N2 fixation (rhizobial,

endorhizal, associative)Nitrifying bacteriaDenitrifying bacteria

Pseudomonads - nutrient mobilization, disease suppression

- Gram positiveOverall: decomposition of complex organic materials (relative to

Gram -)stress resistance

Actinobacteria - disease suppression (antibiotic synthesis); residue decomposition

- Anaerobic bacteria function in saturated microenvironment - denitrification, sulfate

reduction;Indicators of soil compaction or aeration problems - related to DB

values

Antifungal activity of bacterial isolates

Soil Microbial Categories:4. “Total Fungi” -

(ng/g; nmol/g, pmol/g, mol%)

- Overall: Decomposers of most complex organic substrates and xenobiotics

AmmonificationSoil aggregationPathogen suppression

- Mycorrhizal fungi - plant symbiosis; mineral and organic P mobilization & transport to plant;

improves root water uptake (impart drought resistance

to plant); mineralize N, S, K;

Pathogen suppression;‘Glomalin’ deposits in rhizospheres are criticalsinks for C storage and forstable soil aggregation

Faculty of Biology Genetics, University of Munich

Soil Microbial Categories:5. “Protozoa or Protists” -

(ng/g; nmol/g, pmol/g, mol%)

- Overall: Nutrient cycling

- Predatory - ‘microbial turnover’ - mineralize organic, microbial N

maintains balanced microbial community

Soil Microbial Categories:6. Algae -

(ng/g; nmol/g, pmol/g, mol%)

- Overall: Nutrient cycling; photosynthesis (C supply to soil and microbial community); extracellular polysaccharides bind soil particles, increase aggregate stability, formation of erosion-

resistant soil crusts; food source for predatory protozoa, nematodes

- ‘microbial turnover’

Nostic sp.

Location of symbiotic bacteria in intestines of their respective nematode hosts. (A) Xenorhabdus nematophila cells located in the intestinal vesicle of Steinernema carpocapsae infective juveniles. (B) Photorhabdus luminescens cells located in the anteriors and midintestine of Heterorhabditis bacteriophora nematodes. The bacteria are denoted by arrows.

Soil Microbial Categories:7. NematodesImportant in regulating bacterial and fungal communities; cycle N; primary decomposers of coarse organic materials

Cysts on soybean root

Soybean Cyst Nematode

Eggs

Stylet (feeding structure)

SCN egg attacked by soil fungusCysts on Roots

“Microarthropod” – Collembola – “springtail”≤ 2.0 mm length

Soil Microbial Categories:8. Soil Insects – MicroarthropodsFragment coarse organic residues, preparing it for subsequent decomposition by microbes; aid soil structure; feed on plant pathogenic fungi

Soil Microbial Categories:9. Earthworms

Fragment coarse organic residues, preparing it for subsequent decomposition by microbes; aid soil structure by increasing porosity and aggregation; concentrates soil N and P in castings; provides gut habitat for microbes involved in mineral cycling;**Sensitive to changes in soil management

Soil Microbial Categories:10. “Fungi-Bacteria Biomass Ratio” (F:B) -

Implication: Ratios reflect

ecosystem:F:B = 0.3:1 - 0.8:1 =>

row crops, vegetables = 10:1 - 50:1 => orchards, woody plants

Fungi may be associated with higher soil NH4;

Bacteria associated with high soil NO3

Certain plants favor specific type of Ni.e., woody plants – NH4

annual plants - NO3

Willow prefers N as NH4

Soil Microbial Categories:11. “Stress Ratios” -i.e., monounsaturated PLFA : polyunsaturated PLFA or “saturated PLFA : monounsaturated PLFA”

higher ratio suggests microbial community subjected to some stress; may include plant stress

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Microbial diversity components for management practices on claypan soil, Novelty, MO - 2009 (Buffers established in 1997)

*Microbial biomass did not differ significantly among management practices

Unger et al. 2013. Agroforestry Systems 87:395-402.

Soil Enzyme Activities as Indicators of Soil Quality

Enzyme activities seem to be sensitive in discriminating among soil management treatment effects – more dynamic measure vs SOM

Long-term Cropping SitesRotationsTillage Systems Forest ecosystems -- little effort

Clear-cut sites -- phosphatase activity decreased under compaction vs 'rehabilitated site'

Phosphatase activity inversely proportional to Bulk DensitySuggest soil enzyme activity used by forest managers to identify beneficial

management practices before investigating subsequent tree growth Selected Soil Enzymes — potential SQ indicators

**Enzymes representing critical soil biological processes should be selectedEnzymes procedures simple, rapid, can be routinely performed - IN THE LABSensitive to temporal changes in soils due to environment or managementInformation of long-term effects of management can be provided

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Example of activity indicator detecting change due to management well in advance of SOC indicator

10 20 30 40 50 60 700

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f(x) = 3.96876004673475 x + 42.2186893195957R² = 0.628606541908316

GLUCOSAMINIDASE X SOC

SOC (g/kg soil)

Gluc

o Ac

tivity

(PN

P/g

soil)

Relationship of soil microbial activity to SOC content in Sharpsburg silt loamOrganic farm site in Clay County, MO - SOM annually built up thru organic amendments

Continuous vegetative cover

Tilled, not managed

Expect relationship to improve using specific C fractions vs broader SOC values

Kremer & Hezel, 2013. Renewable Agric. & Food Syst. 28:245-254.

Management Inferences from Soil Health AnalysisMycorrhizae

PLFA biomarker for mycorrhizae

Lehman et al., 2012

Cover crop composition (mix) stimulates soil mycorrhizae populations for colonization of subsequent cash crops